I do believe those get broken. There's a list of concommands around here somewhere you can fire off once you've activated Following in his Footsteps that supposedly fix it, but I waited too long on my game. I fired them off immediately before beginning Take it Back!, apparently that's too late.
The only other trouble I had with the main quest was during the FO3/Broken Steel transition, and that I can trace down to a huge clusterfuck between my custom race, CRBSOR, TTW and Bethesda's stupid scripting that kicks Broken Steel into gear. I got around it using player.matchrace commands a couple of times, which avoided breaking my perks as showracemenu is apt to do.
What I did there: I matched race with Sentinal Lyons first, then had to set my age to an adult for some reason. Apparently she's a kid? After that I activated purifier. Woke up in the Citadel as intended. At that point I saved, exited, popped the GECK open and went rummaging. Happy times, there's a test NPC the race mod author made still present! With that baseID in hand I loaded back in, spawned that NPC, used player.matchrace again, disabled that NPC, and done. Bit of a PITA but it worked.
Patrollin' the Capitol Wasteland makes me wish for a nuclear winter...